Contacts of the helix formed by residues 46 - 63 (chain A) in PDB entry 2K1S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASN* 2.7 30.6 + - - +
36A VAL* 3.6 16.6 - - - +
37A THR 3.5 12.5 + - - +
38A PHE 3.2 22.4 + - - -
39A ASP* 3.6 23.0 + - + +
44A THR 3.1 6.1 + - - +
45A LEU* 1.3 72.4 - - - +
47A PRO* 1.3 77.5 - - + +
48A ALA* 4.3 12.1 - - + +
49A GLY 2.9 11.7 + - - +
50A ALA* 2.8 20.8 + - - +
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Residues in contact with PRO 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU 4.0 1.8 - - - +
46A LYS* 1.3 87.4 - - + +
48A ALA* 1.3 58.1 + - - +
50A ALA* 3.4 7.2 + - + +
51A ASN* 2.8 31.4 + - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.4 4.7 - - - +
46A LYS* 3.2 15.1 - - + +
47A PRO* 1.3 78.3 - - - +
49A GLY* 1.3 58.7 + - - +
51A ASN* 3.3 9.4 + - - +
52A THR* 3.0 32.6 + - - -
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 4.8 3.5 - - - +
36A VAL 3.6 20.0 + - - -
37A THR* 4.3 13.9 - - - -
45A LEU* 5.7 0.4 - - - -
46A LYS* 2.9 8.2 + - - +
48A ALA* 1.3 76.1 - - - +
50A ALA* 1.3 55.6 + - - +
52A THR* 3.1 7.7 + - - -
53A LEU* 2.7 44.5 + - - +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.9 15.3 - - + +
46A LYS 2.8 15.7 + - - +
47A PRO* 3.7 8.5 - - + +
49A GLY* 1.3 75.7 - - - +
51A ASN* 1.3 53.4 + - - +
53A LEU* 3.7 13.0 - - + +
54A THR* 2.8 37.1 + - - -
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR* 6.3 1.0 - - - +
47A PRO 2.8 18.6 + - - +
48A ALA* 3.4 7.9 + - - +
50A ALA* 1.3 77.8 - - - +
52A THR* 1.3 62.3 + - - +
54A THR* 3.3 11.1 - - - +
55A GLY* 3.2 15.9 + - - -
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MET* 3.5 31.6 - - + +
17A THR* 3.8 23.5 + - + +
19A VAL* 3.5 21.5 - - + -
32A MET* 4.1 9.9 - - + -
48A ALA 3.0 15.5 + - - -
49A GLY* 3.5 7.4 - - - -
51A ASN* 1.3 76.9 + - - +
53A LEU* 1.3 64.7 + - - +
55A GLY* 3.0 12.9 + - - +
56A VAL* 3.0 15.7 + - + +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 3.9 27.8 - - + -
37A THR* 4.9 3.4 - - + -
45A LEU* 3.9 28.3 - - + -
49A GLY 2.7 31.1 + - - +
50A ALA* 3.7 8.1 - - - +
52A THR* 1.3 71.8 - - - +
54A THR* 1.3 58.8 + - - +
56A VAL* 3.3 8.5 + - + +
57A ALA* 2.9 28.8 + - - +
94A VAL* 3.9 31.0 - - + -
97A ALA* 4.0 25.1 - - + -
98A LEU* 3.7 9.8 - - + +
136A ILE* 4.7 5.4 - - + -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 2.8 19.5 + - - +
51A ASN* 3.3 15.0 - - - +
52A THR 3.1 0.2 - - - -
53A LEU* 1.3 74.3 - - - +
55A GLY* 1.3 60.5 + - - +
57A ALA* 3.2 7.3 + - - +
58A MET* 2.8 46.4 + - + +
101A GLN* 3.1 35.9 + - + +
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 4.3 11.4 - - - +
14A MET* 4.6 8.3 - - - -
51A ASN 3.2 6.6 + - - -
52A THR* 3.0 8.9 + - - -
54A THR* 1.3 79.1 - - - +
56A VAL* 1.3 59.8 + - - +
58A MET* 3.2 17.3 + - - +
59A VAL* 3.2 27.3 + - - +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 5.1 2.0 - - + -
14A MET* 3.6 19.7 - - + +
19A VAL* 6.1 1.6 - - + -
30A LEU* 4.2 25.6 - - + -
32A MET* 5.5 2.7 - - - -
52A THR* 3.0 18.4 + - + +
53A LEU* 3.5 17.9 - - + +
55A GLY* 1.3 74.2 - - - +
57A ALA* 1.3 63.1 + - - +
59A VAL* 3.1 10.9 + - + +
60A LEU* 3.0 43.0 + - + +
98A LEU* 4.6 6.1 - - + -
136A ILE* 4.5 19.5 - - + -
138A LEU* 5.1 2.7 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU 2.9 18.3 + - - +
54A THR 3.5 4.9 - - - +
56A VAL* 1.3 76.8 - - - +
58A MET* 1.3 62.6 + - - +
60A LEU* 3.2 7.3 + - - +
61A LYS* 3.0 28.8 + - - +
98A LEU* 3.9 6.7 - - + +
101A GLN* 3.8 28.9 - - + -
103A VAL* 3.8 24.0 - - + +
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Residues in contact with MET 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 4.0 19.5 - - - +
54A THR* 2.8 32.4 + - + +
55A GLY* 3.3 16.8 - - - +
56A VAL 3.2 0.2 - - - -
57A ALA* 1.3 76.4 - - - +
59A VAL* 1.3 56.9 + - - +
61A LYS* 3.0 15.3 + - + +
62A GLU* 2.9 32.9 + - - +
101A GLN* 5.9 2.0 - - + -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLN* 4.3 29.2 - - + +
9A LYS* 4.7 9.6 - - + -
10A LEU* 3.7 34.3 - - + -
13A LYS* 3.6 17.3 - - + +
55A GLY 3.3 15.0 - - - +
56A VAL* 3.1 6.4 + - + +
58A MET* 1.3 74.4 - - - +
60A LEU* 1.3 60.5 + - + +
62A GLU* 3.1 19.6 + - - +
63A TYR* 3.0 31.8 + - + +
138A LEU* 5.9 3.1 - - + -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLN* 5.7 0.2 - - - +
56A VAL* 3.0 28.0 + - + +
57A ALA* 3.2 11.0 + - - +
59A VAL* 1.3 78.5 - - + +
61A LYS* 1.3 58.5 + - - +
63A TYR 3.3 9.3 - - - +
64A PRO* 3.9 0.5 - - - +
66A THR* 3.7 18.6 - - + +
68A VAL* 3.8 22.7 - - + -
98A LEU* 3.9 17.9 - - + -
103A VAL* 3.9 24.9 - - + -
107A ARG* 2.8 34.0 + - - +
138A LEU* 3.7 34.1 - - + -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA 3.0 17.6 + - - +
58A MET* 3.0 15.2 + - + +
60A LEU* 1.3 77.8 - - - +
62A GLU* 1.3 64.9 + - + +
63A TYR 3.2 0.6 + - - -
64A PRO* 4.3 9.6 - - - +
101A GLN* 2.8 39.6 + - - +
102A GLY* 3.6 26.1 - - - +
103A VAL* 5.1 2.2 - - + -
107A ARG* 5.4 1.1 - - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 2.6 36.7 + - - +
13A LYS* 2.7 31.2 + - - -
58A MET* 2.9 15.3 + - + +
59A VAL* 3.1 23.7 + - - +
61A LYS* 1.3 78.2 - - + +
63A TYR* 1.3 78.4 + - + +
64A PRO* 3.8 5.8 - - - +
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A TYR* 3.2 38.1 - + + +
5A VAL* 3.2 29.2 - - + +
6A GLN* 3.4 37.7 - - + +
9A LYS* 3.2 38.3 - - + -
59A VAL* 3.0 11.6 + - + +
60A LEU 3.3 8.6 - - - +
62A GLU* 1.3 94.6 - - + +
64A PRO* 1.3 56.2 - - - +
65A LYS 3.2 4.7 + - - -
66A THR* 2.8 28.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il